Johnny Sokko and His Flying Robot (1967)
(TV Series)
Both Giant Robo and the Iron Giant are thinking robots who befriend little boys who command them (Daisaku Kusama/Johnny Sokko and Hogarth Hughes, respectively), both were originally created as weapons of destruction, and both sacrifice themselves to save Earth in similar manners (both fly out into space and hurtle into a meteor and nuclear missile, respectively) in the respective finales.

MacArthur (1977)
When Kent Mansley calls General Rogard from the Hughes residence, the shot in which Rogard picks up the phone is an almost identical recreation of a scene from 1977's MacArthur, in which General MacArthur picks up a phone while watching a black-and-white western film.

Aliens (1986)
When he tapes the flashlight to the gun before going after the giant, it's a reference to the scene in Aliens where Sigourney Weaver's character tapes together the gun and some other things before going after Newt in the queen alien's lair.

Justice League: I Am Legion (2005)
(TV Episode)
The robot that initially attacks Luthor, Polaris and The Key is virtually identical in silhouette (if not full appearance) to the titular character of The Iron Giant

Take (2008)
Mary paraphrases Hogarth's line by saying "I don't think I'm smarter than they are. I just did the homework. If they did they homework they could answer the questions and I could have had a break"

Super 8 (2011)
The scene were the car with the kids in pass the army cars is in reference to a scene in The Iron Giant were the same thing happens. Also, the block shapes that form the aliens ship are very similar to the parts of the giant in the terms of their 'remote control properties'.

Duck Dodgers: Till Doom Do Us Part (2005)
(TV Episode)
When Roboto reveals how Duck Dodgers has wronged him in the past, it features an exchange between them that spoofs the one between The Iron Giant and Hogarth towards the end of the film.